Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations (Q26822885)

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English	Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations	scientific article

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scholarly article

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Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations (English)

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molecular dynamics simulation

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protein folding

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author name string

Stefano Piana

1

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John L Klepeis

2

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David E Shaw

3

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language of work or name

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publication date

February 2014

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Current Opinion in Structural Biology

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24

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98-105

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On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

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CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data

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Improved side-chain torsion potentials for the Amber ff99SB protein force field

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Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

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Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

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Temperature and pressure denaturation of chignolin: folding and unfolding simulation by multibaric-multithermal molecular dynamics method

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Folding of Top7 in unbiased all-atom Monte Carlo simulations.

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How to derive a protein folding potential? A new approach to an old problem

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Comparison of protein force fields for molecular dynamics simulations

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Enhanced sampling algorithms

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Contact potential that recognizes the correct folding of globular proteins

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Force field bias in protein folding simulations

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Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

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Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water

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How robust are protein folding simulations with respect to force field parameterization?

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Three force fields' views of the 3(10) helix.

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Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign

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Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

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Discerning the structure and energy of multiple transition states in protein folding using psi-analysis

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Early collapse is not an obligate step in protein folding

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Reproducible polypeptide folding and structure prediction using molecular dynamics simulations

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Sub-microsecond protein folding

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The folding mechanism of BBL: Plasticity of transition-state structure observed within an ultrafast folding protein family

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Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain

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Theory of protein folding

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Transition networks for modeling the kinetics of conformational change in macromolecules

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Targeting biomolecular flexibility with metadynamics

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How, when and why proteins collapse: the relation to folding

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Atomistic molecular simulations of protein folding

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To milliseconds and beyond: challenges in the simulation of protein folding

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Rapid Cooperative Two-state Folding of a Miniature α–β Protein and Design of a Thermostable Variant

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Pathways for protein folding: is a new view needed?

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Is there a unifying mechanism for protein folding?

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Calorimetric analysis of lambda cI repressor binding to DNA operator sites

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Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G.

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Reversible dimerization of acid-denatured ACBP controlled by helix A4.

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The Native GCN4 Leucine-Zipper Domain Does Not Uniquely Specify a Dimeric Oligomerization State

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Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding

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Thermodynamic characterization of the folding equilibrium of the human Nedd4-WW4 domain: at the frontiers of cooperative folding.

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Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

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Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

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Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism.

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Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

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Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

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Crystal structure of a ten-amino acid protein

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Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

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Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data

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Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models

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Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

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Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles

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Folding simulations of the A and B domains of protein G

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Confinement-induced states in the folding landscape of the Trp-cage miniprotein

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Atomistic description of the folding of a dimeric protein

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Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

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Computer simulation of protein folding

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Mapping the transition state and pathway of protein folding by protein engineering

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Atom-by-atom analysis of global downhill protein folding

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Behind the folding funnel diagram

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Capturing the essence of folding and functions of biomolecules using coarse-grained models

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Challenges in protein folding simulations: Timescale, representation, and analysis

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Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

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Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

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On developing coarse-grained models for biomolecular simulation: a review

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Microsecond folding experiments and simulations: a match is made

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Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

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Random-coil behavior and the dimensions of chemically unfolded proteins

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Phi-value analysis by molecular dynamics simulations of reversible folding

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Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

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Folding helical proteins in explicit solvent using dihedral-biased tempering

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Energy landscape of knotted protein folding

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Protein folding kinetics and thermodynamics from atomistic simulation

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Atomic-level description of ubiquitin folding

1 reference

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Atomic-Level Characterization of the Structural Dynamics of Proteins

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